[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

[Mark Abraham]

Hi,

Why would you do some equilibration, then some further equilibration, and
then start from the point before the further equilibration?

Mark

On Wed, Mar 30, 2016 at 8:12 PM Pradip Kaur <kaur.pradip253 at gmail.com>
wrote:

> but i have one question  when i m running md.mdp which file should i use as
> input file ,posre_npt.pdb or posre_nvt.pdb ?
>
> On 30 March 2016 at 23:40, Pradip Kaur <kaur.pradip253 at gmail.com> wrote:
>
> > thanks so much
> >
> > On 30 March 2016 at 21:33, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> The purpose of these equilibration phases is to allow the system to
> relax
> >> to the desired temperature and pressure. Since you observed that this
> >> happened before starting your production MD ;-) then there's no issue.
> But
> >> in many cases you'll have an easier life if you do it the other way
> >> around.
> >>
> >> Mark
> >>
> >> On Wed, Mar 30, 2016 at 5:23 PM Pradip Kaur <kaur.pradip253 at gmail.com>
> >> wrote:
> >>
> >> > i have run posre_npt.mdp first and then posre_nvt.mdp by mistake but
> now
> >> > going through gromacs manual i found that posre_nvt.mdp is first run
> and
> >> > then posre_npt.mdp, but i have already started  md.mdp run with
> >> > posre_nvt.pdb (which was last generated pdb file after mdrun of
> >> > posre_nvt.mdp ) there is no error till now, should i need to stop my
> >> run or
> >> > continue with it ?
> >> > --
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